Metadata-Version: 2.1
Name: bdgenomics.mango.pileup
Version: 0.0.6a1
Summary: bdgenomics.mango.pileup
Home-page: http://jupyter.org
Author: Alyssa Morrow
Author-email: akmorrow@berkeley.edu
License: UNKNOWN
Description: # bdgenomics.mango.pileup
        
        bdgenomics.mango.pileup is a Jupyter widget that allows users to view genomic reads, variants and features in a Jupyter notebook or in Jupyter lab version >2.0.
        bdgenomics.mango.pileup builds off of [pileup.js](https://github.com/hammerlab/pileup.js).
        
        ## Installation
        
        ### from pip:
        
            $ pip install bdgenomics.mango.pileup
        
        #### Enable widgets for Jupyter notebook:
        
            $ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup  # can be skipped for notebook version 5.3 and above
        
        #### Install widgets for jupyter lab:
        
            $ jupyter labextension install bdgenomics.mango.pileup
        
        ## Running Examples
        
            $ First run installation, explained above.
            $ cd examples
            $ jupyter notebook
        
        Or run in Jupyter lab:
        
            $ jupyter lab
        
        ### from Source:
        
        For a development installation (requires npm (version >= 3.8) and node (version >= 4.0)):
        
            $ git clone https://github.com/bdgenomics/mango
            $ cd mango-pileup
            $ rm -r bdgenomics/mango/pileup/static
        
        Install bdgenomics.mango.pileup:
        
            $ pip install -e .
            $ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
            $ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup]
        
        Note for developers: the --symlink argument on Linux or OS X allows one to modify the JavaScript code in-place. This feature is not available with Windows.
        
        
        To install the JupyterLab extension, install the Package, the Jupyter widgets extension, and the bdgenomics.mango.pileup extension:
        
        
            $ pip install -e .
            $ cd bdgenomics/mango/js/
            $ jupyter labextension install @jupyter-widgets/jupyterlab-manager # install the Jupyter widgets extension
            $ jupyter labextension install .
        
        
        #### Testing:
        
        mango-pileup has a Makefile with a ``test`` command to run tests for python and javascript:
        
            $ make test
        
Keywords: ipython,jupyter,widgets,pileup,genome
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: IPython
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Multimedia :: Graphics
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Description-Content-Type: text/markdown
